Not like it seems
by johnliz4ever
Summary: Not everything is what it seems. JohnElizabeth


Disclaimer: Don't own Stargate Atlantis

Note: No idea where this came from.

* * *

John turned the corner to where Elizabeth's quarters were, his hope was to catch her early and in a good mood so she'd lift the ban on his team going off world. 

On their last off world mission, they'd met with a tiny technical problem on Atlantis and Elizabeth had ordered them to come back until it could be dealt with. John, being John, had decided that a technical problem on Atlantis wouldn't affect them off world so he disobeyed her order and carried on, ordering his team to do the same.

Ford had blindly followed the order, Teyla, after voicing her opinion that he should not overrule Elizabeth's authority finally gave up and followed his order. Rodney had been rather vocal in the fact that he wasn't military and didn't have to follow John's orders. He'd been about to dial the 'Gate when a strange power reading got his attention, he than decided that John was right. How could a technical problem on Atlantis cause problems off world?

They found out when the natives of the planet attacked them and they couldn't dial Atlantis, after a lot of cursing and shooting they dialled the Alpha site, which was strangely deserted. They went into the camp and found a radio transmission from Elizabeth, who sounded rather pissed, on the MALP

"_SGA-1. If you'd listened to my order you wouldn't be in this predicament. The technical problems I told you about have increased. We were unaware of what would happen if it did, when Dr Zelenka finally told me I decided that this would be the best cause of action.  
I have ordered the 'Gate to be shut down and cut off from all power sources until we can find a solution to the problem. I won't bore you with the details but you will not be able to dial Atlantis until I allow the 'Gate to be activated again. Thankfully, everyone else respected my order so you are the only ones off world. I don't know how long it will take to fix the problem, but hopefully it will be soon. And when you do get back, we are going to have a long talk. For the time being stay where you are"_

The team had been scared by how pissed Elizabeth sounded and several said that they shouldn't go back if they valued their lives. It was said in a joke but John knew he would be on the receiving end of most of the blame.

Three days later the 'Gate finally activated and it was Weir telling them that all problems had been sorted and they were able to dial the Stargate to Atlantis.

When they got back, Elizabeth had immediately called a meeting, despite the fact the team were tired, hungry and smelt bad. She saw it as almost a punishment.

The problem had been a virus in the computer system and since the computer system was connected to the dialling computer they knew the Stargate could get infected which resulted in Weir ordering the Stargate to be shut off.

When John asked her why she didn't tell him that before Elizabeth had got, rather angry again

"_Major, when I tell you that there is a technical problem that is as yet unidentified I expect you to obey my orders, whatever they are. Now we didn't know that the Stargate could get infected until an hour after we connected you. We tried to contact you again but we couldn't. I couldn't risk the 'Gate getting infected, if it did we may have lost all 'Gate activity period. I sent you that transmission to the Alpha site and then shut down the 'Gate until the problem was solved.  
You got yourself and your team into that problem Major, don't even try to shift the blame.  
All of you are suspended from off world mission's until I see fit. Dismissed"_

Afterwards each had said how pissed Elizabeth had seemed and how they'd never seen her like that before. Teyla and Ford and gone to the mainland for a few days and McKay had decided to catch up on what he'd missed.

John had tried to be good and stay out of Elizabeth's way. He'd made a hell of a mistake and was paying for it. She'd relived him of duty until further notice and put Bates in charge of the military aspect temporarily, which Bates loved boosting about. She'd made her anger know by avoiding him as well.

John had decided four days into his suspension that he was sick of Bates walking around like he owned the place and was sick of the fact he and Elizabeth were no longer on speaking terms.

So that's were he was now, going to Elizabeth to grovel.

As he took the final step into the corridor, he stopped dead in his tracks.

He could see Elizabeth with her arms around Carson, the two of them wrapped in a hug. John couldn't help but feel a sting of jealousy. It was only a hug though, he'd hugged Carson before. John was about to start walking again when he saw Carson kiss Elizabeth on the cheek, whisper something to her and than walk off.

John stood stunned for a moment and quickly turned into the corridor he walked from. He leant against the wall and sighed, okay probability not as innocent as he thought. He was about to leave the corridor when he banged into someone.

He looked down to see who it was, only to discover it was Elizabeth.

"Dr Weir"

Elizabeth eyed him suspiciously

"Major, what are you doing awake so early?"

John sputtered something about taking a walk

"Near my quarters"

John smiled and sighed

"I admit; I was coming to grovel. I'm sorry about what happened and I take full responsibly. And I'm just sorry"

Elizabeth nodded.

"Apology accepted Major"

John nodded and was about to turn away when he stopped and looked at Elizabeth.

"Just so you know. I kinda know about you and the doc."

Elizabeth stared at him

"What?"

John continued completely oblivious to the confusion on his face.

"I wasn't snooping…I just saw the two of you. I'm happy for you, you deserve to be happy. I'm happy for you"

"John…"

John cut in

"Don't worry I won't tell anyone, this is your business"

Elizabeth grabbed his arms and stopped him from fidgeting

"Major, it would help if I knew what you were talking about"

John shifted uncomfortably

"You and Beckett, I just saw…"

Elizabeth cut in, slightly amused

"…what you saw was a hug between two good friends. I had some blood tests done yesterday, I thought I had a problem; Carson's just got the results and thought I'd want to know straightaway. I'm fine by the way, nothing to worry about. That was what the hug was for."

John stood, silently stunned for a moment before responding.

"Oh, so you're not…"

Elizabeth shook her head

"No we're not."

John smiled, a little embarrassed.

"Oh, because you know there's no rule forbidding it. It's like civilian and military, there's no rule against it."

Elizabeth nodded

"I know, although it is frowned up"

Elizabeth was still clearly amused by how John was acting.

"Who listens to those rules anymore?"

Elizabeth nodded and walked past John; she stopped and turned round facing him.

"I'm going to the mess hall for some breakfast, would you care to join me."

John nodded and ran to catch her up.

Fin.


End file.
